From: gmungoc Date: Thu, 10 Sep 2020 11:28:47 +0000 (+0100) Subject: JAL-2422 comments updated re ALTLOC handling X-Git-Tag: Release_2_11_2_0~37^2~7 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=15684417a64007046f10d193d5c9363be8f88ea7;p=jalview.git JAL-2422 comments updated re ALTLOC handling --- diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java index b7d9ce3..d0c5671 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java @@ -20,15 +20,15 @@ */ package jalview.ext.rbvi.chimera; +import java.awt.Color; +import java.util.Arrays; +import java.util.List; + import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.util.ColorUtils; -import java.awt.Color; -import java.util.Arrays; -import java.util.List; - /** * Routines for generating ChimeraX commands for Jalview/ChimeraX binding */ @@ -132,6 +132,10 @@ public class ChimeraXCommands extends ChimeraCommands * Returns the range(s) formatted as a ChimeraX atomspec, for example *

* #1/A:2-20,30-40/B:10-20|#2/A:12-30 + *

+ * Note there is no need to explicitly exclude ALTLOC atoms when + * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a + * change from Chimera) * * @return */ @@ -153,7 +157,6 @@ public class ChimeraXCommands extends ChimeraCommands // TODO @P if RNA - add nucleotide flag to AtomSpecModel? sb.append("@CA"); } - // todo: is there ChimeraX syntax to exclude altlocs? } return sb.toString(); }